BOL: Wire posts tagged with 'Fasta'

Wire post by BioStar

BioStar — Mon, 22 Jan 2024 03:25:18 -0600

Delete all the headers from multifasta file $ awk 'BEGIN {print ">"ARGV[1]};!/^>/{print}' test.fa #fasta #delete #header #multifasta

Wire post by Rahul Nayak

Rahul Nayak — Fri, 21 Jan 2022 21:14:54 -0600

Fold the FASTA sequences with length $ fold -w 100 genome.fa #Fasta #Genome #Fold #Break #Length

Wire post by LEGE

LEGE — Thu, 02 Sep 2021 06:41:33 -0500

Count number of fasta sequence $ awk '/^>/ { f = !a[$0]++ } f' aaaa.fa > bbbb.fa #count #fasta #oneliner

Wire post by Jit

Jit — Tue, 23 Mar 2021 07:26:49 -0500

Multi fasta to single fasta files $ perl -ne 'if (/^>(\S+)/) { close OUT; open OUT, ">$1.fasta" } print OUT' genome.fasta #Multi-fasta #fasta #multi #genome #files

Wire post by Neel

Neel — Fri, 29 Nov 2019 22:14:54 -0600

Perl onliner to add string to each of the fasta header. $ perl -p -e 's/^(>.*)$/$1-origin/g' in.fasta > out.fasta #String #Header #Fasta

Wire post by Neel

Neel — Mon, 25 Nov 2019 22:26:37 -0600

Multifasta 2 singlefasta cat toy.fasta| awk '{ if (substr($0, 1, 1)==">" {filename=(substr($0,2) ".fa")} print $0 > filename }' #Split #fasta #multifasta

Wire post by Neel

Neel — Fri, 15 Nov 2019 23:13:24 -0600

#Rename the #fasta #header and #keep first $ perl -ne 'if (/^(>\S+)/){print "$1\n";}else{print $_;}' realTestDATA.fa > realTestDATA_headerCorrected.fa #Perl

Wire post by Jit

Jit — Mon, 11 Feb 2019 18:01:41 -0600

Extract fasta with pattern $ perl -n -e '$on=(/^>(A)/) if (/^>/); print $_ if ($on);' pilonCor_round1.fasta > A_set.fa
#Pattern #Extract #Fasta

Wire post by Rahul Nayak

Rahul Nayak — Mon, 11 Feb 2019 06:11:41 -0600

One liner to remove the description information from a fasta file and just keep the identifier $ perl -p -i -e 's/>(.+?) .+/>$1/g' sample1.fa #clean #header #fasta

Wire post by Neel

Neel — Sun, 27 Jan 2019 14:56:30 -0600

(smrttools) ➜ allBam for i in *.bam; do bamtools convert -format fasta -in $i -out $i.fasta; done #Convert #fasta

Wire post by Rahul Nayak

Rahul Nayak — Thu, 20 Dec 2018 13:18:03 -0600

Add number in fasta header $ awk '/^>/{$0=$0"_"(++i)}1' infile.fa #fasta #header #add #number #count

Wire post by Jit

Jit — Fri, 02 Nov 2018 09:23:44 -0500

Rename the fasta header perl -ane 'if(/\>/){$a++;print ">LR$a\n"}else{print;}' allPacBio_clean.fa > allPacBio_clean_shortName.fa
#fasta #header #rename

Wire post by Jit

Jit — Mon, 22 Oct 2018 09:17:39 -0500

Tab file to FASTA file $ awk '{print ">"$1"\n"$2}' allSeq_tm.txt > allSeq_tm.fa #Fasta #Tab #Convert #Tab2Fasta

Wire post by Neel

Neel — Mon, 01 Oct 2018 09:03:12 -0500

Multifasta to singleline fasta. $ awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa #Multi #Single #Fasta #Convert

Wire post by BioStar

BioStar — Sat, 22 Sep 2018 07:03:57 -0500

Remove empty line from fasta. $ sed -i '/^$/d' standard_output.final.scaffolds_online.fasta #Empty #Fasta #Remove